{"action":"created","issue":{"url":"https://api.github.com/repos/NBISweden/IgDiscover/issues/40","repository_url":"https://api.github.com/repos/NBISweden/IgDiscover","labels_url":"https://api.github.com/repos/NBISweden/IgDiscover/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/NBISweden/IgDiscover/issues/40/comments","events_url":"https://api.github.com/repos/NBISweden/IgDiscover/issues/40/events","html_url":"https://github.com/NBISweden/IgDiscover/issues/40","id":204241370,"number":40,"title":"Spawn only as many igblastn processes as cores","user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars3.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"labels":[{"id":529168784,"url":"https://api.github.com/repos/NBISweden/IgDiscover/labels/major","name":"major","color":"ededed","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-19T09:48:11Z","updated_at":"2017-04-19T21:35:41Z","closed_at":null,"body":"Currently, in the igblast subcommand, a new igblastn process is spawned for each chunk of reads that is processed. This is quite some overhead.\r\n"},"comment":{"url":"https://api.github.com/repos/NBISweden/IgDiscover/issues/comments/295453994","html_url":"https://github.com/NBISweden/IgDiscover/issues/40#issuecomment-295453994","issue_url":"https://api.github.com/repos/NBISweden/IgDiscover/issues/40","id":295453994,"user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars3.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"created_at":"2017-04-19T21:35:41Z","updated_at":"2017-04-19T21:35:41Z","body":"I’ve tried to implement this and it is more difficult than I thought. If there is only a single `igblastn` process per core that continually gets fed new sequences, then its output also needs to be collected continuously. It seems this cannot be done reliably without deadlocks unless we spawn yet another process to collect the results (one process writes to `igblastn` stdin, the other reads from `igblastn` stdout).\r\n\r\nThis may not be necessary in the near future with better support for multithreading in IgBLAST."}}
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